RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 02-Jun-2021 15:21:31 as follows:

raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53007/2_msa/P53007_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53007/3_mltree/P53007.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53007/4_raxmlng_ancestral/P53007 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622636491
  tip-inner: ON
  pattern compression: OFF
  per-rate scalers: OFF
  site repeats: OFF
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53007/2_msa/P53007_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 311 sites

WARNING: Sequences tr_M3XXI9_M3XXI9_MUSPF_9669 and tr_A0A2Y9ISB4_A0A2Y9ISB4_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_J3K2C3_J3K2C3_COCIM_246410 and tr_E9D1C7_E9D1C7_COCPS_443226 are exactly identical!
WARNING: Sequences tr_J3K2C3_J3K2C3_COCIM_246410 and tr_A0A0J6YMZ0_A0A0J6YMZ0_COCIT_404692 are exactly identical!
WARNING: Sequences tr_J3KKN1_J3KKN1_COCIM_246410 and tr_A0A0J7AXI7_A0A0J7AXI7_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6Q6N9_B6Q6N9_TALMQ_441960 and tr_A0A093VXJ7_A0A093VXJ7_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2W206_B2W206_PYRTR_426418 and tr_A0A2W1H5A9_A0A2W1H5A9_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_B2W8M5_B2W8M5_PYRTR_426418 and tr_A0A2W1F2Q9_A0A2W1F2Q9_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_G3QTN4_G3QTN4_GORGO_9595 and tr_H2QL82_H2QL82_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QTN4_G3QTN4_GORGO_9595 and tr_A0A2R8Z7R9_A0A2R8Z7R9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G2XHD1_G2XHD1_VERDV_498257 and tr_A0A0G4LFK2_A0A0G4LFK2_9PEZI_100787 are exactly identical!
WARNING: Sequences tr_B5DVX7_B5DVX7_DROPS_46245 and tr_B4GME5_B4GME5_DROPE_7234 are exactly identical!
WARNING: Sequences tr_B8NVA1_B8NVA1_ASPFN_332952 and tr_A0A1S9DII3_A0A1S9DII3_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179V363_A0A179V363_BLAGS_559298 and tr_C5GM79_C5GM79_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_C6HC07_C6HC07_AJECH_544712 and tr_F0UB45_F0UB45_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_A0A0I9N888_A0A0I9N888_BRUMA_6279 and tr_A0A0N4TM19_A0A0N4TM19_BRUPA_6280 are exactly identical!
WARNING: Sequences tr_A0A0I9N888_A0A0I9N888_BRUMA_6279 and tr_A0A0R3QXS7_A0A0R3QXS7_9BILA_42155 are exactly identical!
WARNING: Sequences tr_A1DIQ8_A1DIQ8_NEOFI_331117 and tr_A0A0S7DKU5_A0A0S7DKU5_9EURO_293939 are exactly identical!
WARNING: Sequences tr_A2QY41_A2QY41_ASPNC_425011 and tr_A0A319A4D2_A0A319A4D2_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_A0A1D5RH47_A0A1D5RH47_MACMU_9544 and tr_A0A2K6C193_A0A2K6C193_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7XFI8_G7XFI8_ASPKW_1033177 and tr_A0A0H5ARK2_A0A0H5ARK2_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_G7XFI8_G7XFI8_ASPKW_1033177 and tr_A0A317V058_A0A317V058_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_F9X7S0_F9X7S0_ZYMTI_336722 and tr_A0A1X7RMY0_A0A1X7RMY0_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G2XRJ9_G2XRJ9_BOTF4_999810 and tr_M7TSY0_M7TSY0_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_E3LS49_E3LS49_CAERE_31234 and tr_A0A261AVN4_A0A261AVN4_9PELO_1503980 are exactly identical!
WARNING: Sequences tr_A8XA18_A8XA18_CAEBR_6238 and tr_A0A2G5UHY1_A0A2G5UHY1_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_B3RQV6_B3RQV6_TRIAD_10228 and tr_A0A369S0J5_A0A369S0J5_9METZ_287889 are exactly identical!
WARNING: Sequences tr_A0A0D2XJI3_A0A0D2XJI3_FUSO4_426428 and tr_N4TW24_N4TW24_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_A0A0D2XJI3_A0A0D2XJI3_FUSO4_426428 and tr_X0DB48_X0DB48_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_A0A0D2XJI3_A0A0D2XJI3_FUSO4_426428 and tr_A0A2H3SY81_A0A2H3SY81_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_A0A0D2XJI3_A0A0D2XJI3_FUSO4_426428 and tr_A0A2H3HHE5_A0A2H3HHE5_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_A0A0D2Y671_A0A0D2Y671_FUSO4_426428 and tr_N4UHI9_N4UHI9_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_A0A0D2Y671_A0A0D2Y671_FUSO4_426428 and tr_A0A2H3GFU5_A0A2H3GFU5_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_A0A0D2Y671_A0A0D2Y671_FUSO4_426428 and tr_A0A365MP06_A0A365MP06_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_F2PQX4_F2PQX4_TRIEC_559882 and tr_A0A059JBN2_A0A059JBN2_9EURO_1215338 are exactly identical!
WARNING: Sequences tr_L2GDX4_L2GDX4_COLFN_1213859 and tr_T0LRA2_T0LRA2_COLGC_1237896 are exactly identical!
WARNING: Sequences tr_S0EJE4_S0EJE4_GIBF5_1279085 and tr_A0A365MZM3_A0A365MZM3_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_A0A0F4GSA1_A0A0F4GSA1_9PEZI_1047168 and tr_A0A1X7S6F3_A0A1X7S6F3_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_A0A0F9XN59_A0A0F9XN59_TRIHA_5544 and tr_A0A2T3ZUH8_A0A2T3ZUH8_TRIHA_983964 are exactly identical!
WARNING: Sequences tr_A0A0F8U829_A0A0F8U829_9EURO_308745 and tr_A0A2T5LLS7_A0A2T5LLS7_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0K0F8I0_A0A0K0F8I0_STRVS_75913 and tr_A0A0N5BWC4_A0A0N5BWC4_STREA_174720 are exactly identical!
WARNING: Sequences tr_A0A0A1NHD4_A0A0A1NHD4_9FUNG_58291 and tr_A0A367IWF9_A0A367IWF9_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A164WX85_A0A164WX85_9HOMO_1314777 and tr_A0A166ENA8_A0A166ENA8_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A1R3RVG1_A0A1R3RVG1_ASPC5_602072 and tr_A0A1R3RVJ9_A0A1R3RVJ9_ASPC5_602072 are exactly identical!
WARNING: Sequences tr_A0A1V8U849_A0A1V8U849_9PEZI_1974281 and tr_A0A1V8TQM0_A0A1V8TQM0_9PEZI_1507870 are exactly identical!
WARNING: Sequences tr_A0A226N3U9_A0A226N3U9_CALSU_9009 and tr_A0A226NTA2_A0A226NTA2_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2H3BPH7_A0A2H3BPH7_9AGAR_1076256 and tr_A0A284RIM9_A0A284RIM9_9AGAR_47428 are exactly identical!
WARNING: Duplicate sequences found: 46

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53007/4_raxmlng_ancestral/P53007.raxml.reduced.phy

Alignment comprises 1 partitions and 311 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 311
Gaps: 11.51 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53007/4_raxmlng_ancestral/P53007.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s)

Parallel reduction/worker buffer size: 1 KB  / 0 KB

[00:00:00] Loading user starting tree(s) from: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53007/3_mltree/P53007.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 78 / 6240
[00:00:00] Data distribution: max. searches per worker: 1

Starting ML tree search with 1 distinct starting trees

[00:00:00] Tree #1, initial LogLikelihood: -123883.241399

[00:00:00 -123883.241399] Initial branch length optimization
[00:00:01 -121550.810294] Model parameter optimization (eps = 0.100000)

[00:00:27] Tree #1, final logLikelihood: -121075.265870


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.260371,0.308699) (0.334787,0.482622) (0.260560,1.419149) (0.144281,2.691092) 
   Base frequencies (model): 
M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 
M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 
M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 
M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 
   Substitution rates (model): 
M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 
M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 
M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 
M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 

Marginal ancestral probabilities saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53007/4_raxmlng_ancestral/P53007.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53007/4_raxmlng_ancestral/P53007.raxml.ancestralStates
Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53007/4_raxmlng_ancestral/P53007.raxml.ancestralTree

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P53007/4_raxmlng_ancestral/P53007.raxml.log

Analysis started: 02-Jun-2021 15:21:31 / finished: 02-Jun-2021 15:22:00

Elapsed time: 29.942 seconds